Monsignor William Lynn became the first U.S. church official convicted of a felony. NBC's Brian Williams reports.

By NBC News and wire services

PHILADELPHIA -- Monsignor William Lynn, the most senior U.S. Catholic clergyman convicted in the church’s decades-long sex abuse scandal, was sentenced on Tuesday to three to six years in jail for covering up child sex abuse by priests in Philadelphia.

The sentence handed down by Judge M. Teresa Sarmina was less than the maximum penalty of seven years in prison for Lynn's conviction on a single count of child endangerment.

Sarmina said the sentence was meant to punish Lynn for protecting "monsters in clerical garb who molested children … to destroy the souls of children, to whom you turned a hard heart."

She added: "You knew full well what was right, Monsignor Lynn, but you chose wrong."

Tim Shaffer / Reuters file

Monsignor William Lynn is shown walking to the courthouse as the jury deliberates on his sexual abuse trial in Philadelphia on June 20.

As the former secretary for the clergy for the Philadelphia Archdiocese, Lynn, 61, was essentially personnel director for 800 priests from 1992 to 2004. He was convicted last month of covering up the allegations by transferring predatory priests to unsuspecting parishes.

Lynn was acquitted of conspiracy and a second endangerment count. The jury deadlocked on a 1996 abuse charge against a co-defendant, the Rev. James Brennan, and prosecutors said Monday that they would retry him.

"I believe that what Lynn did was done by just about every diocese," Terence McKiernan, president of BishopAccountability.org, which tracks priest-abuse cases, told NBCPhiladelphia.com. "In most cases, I think the vicar general was well informed, and also the bishop."

More than 500 U.S. priests have now been convicted of abuse, according to his organization. But Lynn's three-month trial, he said, shows "just how hard it is to demonstrate collusion."

Bishop Robert Finn and the Kansas City diocese face a misdemeanor charge of failing to report suspected child sexual abuse. Both Finn and the diocese have pleaded not guilty, and are set to go on trial next month.

Lynn has been in prison since the June 22 jury verdict, when the trial judge revoked his bail, NBCPhiladelphia.com reported.

Defense lawyers call Lynn a scapegoat for the Philadelphia archdiocese, and plan an appeal. They will also ask that he be released while the lengthy appeals process plays out, NBCPhiladelphia.com reported.

They said the trial was flawed on many levels, starting with the fact Lynn was charged with child endangerment under a law revised in 2007 to include those who supervise the caretakers of children. Lynn had left the archdiocese headquarters in 2004, after serving 12 years as secretary for clergy, and returned to parish work.

"His active, even eager execution of archdiocese policies, carried out in the face of victims' vivid suffering, and employing constant deceit, required a more amoral character, a striving to please his bosses no matter how sinister the business," they wrote in a sentencing memo filed Friday. "At any time during those 12 years, he could have had a moment of conscience."